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Baldock, Brandi

Abstract

DNA-functionalized gold nanoparticles (DNA-NPs) have enormous potential as building blocks for materials due to their ability to specifically recognize and respond to target molecules and surfaces. The ability of DNA aptamers to adopt different conformations and bind either complementary DNA sequences or analyte molecules allows them to mediate nanoparticle assembly or disassembly, generating selective colorimetric responses.
Aptamer-mediated nanoparticle assembly and disassembly is sensitive to the nanoparticle ligand shell composition and structure, yet these topics have not been extensively explored. In this dissertation, a method for determining the ligand shell composition of DNA-NPs is described and a framework for understanding the impact of the DNA assembly arrangement and recognition strand density upon aptamer-mediated nanoparticle assembly and disassembly is developed. Design rules for creating sensors with desired properties are elucidated, leading to creation of sensors with improved detection limits and quantification ranges.
A technique was needed to determine the number of DNA strands of any base composition attached to gold nanoparticles (AuNPs) of any core size. A rapid, convenient and inexpensive method to quantify the number of label-free DNA strands attached to AuNPs was therefore developed. This technique was extended to determine two different DNA sequences bound to AuNPs using UV-visible and fluorescence spectroscopy. Based on the results of quantifying the ligand shells of DNA-NPs functionalized with two sequences, disulfide-terminated DNA non-specifically adsorbs and then rearranges to specifically bind the gold surface.
The position of the AuNPs and DNA strands within DNA-NP assemblies had a profound influence on their ability to assemble and sense adenosine. Assemblies designed for large inter-AuNP spacing were stable but unable to sense adenosine. Assemblies designed for short inter-AuNP spacing were unstable until the DNA ligand shell was diluted.
AuNPs functionalized with the fewest number of aptamers produced assemblies with the lowest detection limit and apparent disassociation constant and the largest analyte quantification range. Increasing the number of aptamer strands per AuNP increased the cooperativity of the AuNP disassembly response to adenosine.
This dissertation includes previously unpublished co-authored material.

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